Literature DB >> 21202598

N,N',N''-Triphenyl-guanidinium 5-nitro-2,4-dioxo-1,2,3,4-tetra-hydro-pyrimidin-1-ide.

P S Pereira Silva1, S R Domingos, M Ramos Silva, J A Paixão, A Matos Beja.   

Abstract

In the title compound, C(19)H(18)N(3) (+.)C(4)H(2)N(3)O(4) (-), the dihedral angles between the phenyl rings and the plane defined by the central guanidinium fragment are in the range 41.3 (1)-66.6 (1)°. The pyrimidine ring of the anion is distorted towards a boat conformation and the nitro group is rotated 11.4 (2)° out of the uracil plane. Hydrogen bonds assemble the ions in infinite helical chains along the b axis.

Entities:  

Year:  2008        PMID: 21202598      PMCID: PMC2961510          DOI: 10.1107/S1600536808014244

Source DB:  PubMed          Journal:  Acta Crystallogr Sect E Struct Rep Online        ISSN: 1600-5368


Related literature

For the non-linear optical properties of 5-nitro­uracil, see: Puccetti et al. (1993 ▶), Youping et al. (1992 ▶). For reports of other triphenyl­guanidine salts, see: Pereira Silva et al. (2006 ▶, 2007a ▶,b ▶), Pereira Silva, Cardoso et al. (2007 ▶). For related literature, see: Allen et al. (1987 ▶); Kemme et al. (1988 ▶); Klement et al. (1995 ▶); Largent et al. (1987 ▶); Pettier & Byrn (1982 ▶); Rao et al. (1995 ▶); Weber et al. (1986 ▶); Zyss et al. (1993 ▶).

Experimental

Crystal data

C19H18N3 +·C4H2N3O4 M = 444.45 Monoclinic, a = 10.7495 (4) Å b = 15.6892 (7) Å c = 15.5624 (7) Å β = 123.456 (3)° V = 2189.74 (18) Å3 Z = 4 Mo Kα radiation μ = 0.10 mm−1 T = 293 (2) K 0.34 × 0.20 × 0.12 mm

Data collection

Bruker APEX2 CCD area-detector diffractometer Absorption correction: multi-scan (SADABS; Sheldrick, 2003 ▶) T min = 0.822, T max = 0.989 47807 measured reflections 5534 independent reflections 2650 reflections with I > 2σ(I) R int = 0.086

Refinement

R[F 2 > 2σ(F 2)] = 0.050 wR(F 2) = 0.154 S = 0.99 5534 reflections 299 parameters H-atom parameters constrained Δρmax = 0.22 e Å−3 Δρmin = −0.17 e Å−3 Data collection: APEX2 (Bruker, 2005 ▶); cell refinement: SAINT (Bruker, 2005 ▶); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▶); molecular graphics: PLATON (Spek, 2003 ▶); software used to prepare material for publication: SHELXL97. Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536808014244/bt2707sup1.cif Structure factors: contains datablocks I. DOI: 10.1107/S1600536808014244/bt2707Isup2.hkl Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C19H18N3+·C4H2N3O4F000 = 928
Mr = 444.45Dx = 1.348 Mg m3
Monoclinic, P21/cMo Kα radiation λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 5110 reflections
a = 10.7495 (4) Åθ = 2.3–21.6º
b = 15.6892 (7) ŵ = 0.10 mm1
c = 15.5624 (7) ÅT = 293 (2) K
β = 123.456 (3)ºBlock, yellow
V = 2189.74 (18) Å30.34 × 0.20 × 0.12 mm
Z = 4
Bruker APEX2 CCD area-detector diffractometer5534 independent reflections
Radiation source: fine-focus sealed tube2650 reflections with I > 2σ(I)
Monochromator: graphiteRint = 0.086
T = 293(2) Kθmax = 28.6º
φ and ω scansθmin = 2.0º
Absorption correction: multi-scan(SADABS; Sheldrick, 2003)h = −14→14
Tmin = 0.822, Tmax = 0.989k = −20→21
47807 measured reflectionsl = −20→20
Refinement on F2Hydrogen site location: inferred from neighbouring sites
Least-squares matrix: fullH-atom parameters constrained
R[F2 > 2σ(F2)] = 0.050  w = 1/[σ2(Fo2) + (0.0713P)2 + 0.1061P] where P = (Fo2 + 2Fc2)/3
wR(F2) = 0.154(Δ/σ)max < 0.001
S = 0.99Δρmax = 0.22 e Å3
5534 reflectionsΔρmin = −0.17 e Å3
299 parametersExtinction correction: SHELXL97 (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.0068 (11)
Secondary atom site location: difference Fourier map
Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s involving l.s. planes.
Refinement. Refinement of F2 against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F2, conventional R-factors R are based on F, with F set to zero for negative F2. The threshold expression of F2 > σ(F2) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F2 are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger.
xyzUiso*/Ueq
O20.82985 (16)−0.17695 (11)0.60642 (13)0.0729 (5)
O40.61600 (16)0.07278 (11)0.59408 (15)0.0968 (6)
O70.7653 (2)0.21285 (11)0.59093 (15)0.0949 (6)
O80.9257 (2)0.19450 (12)0.55194 (16)0.0940 (6)
N10.93683 (17)−0.06007 (12)0.58600 (13)0.0581 (5)
N30.72353 (18)−0.04940 (13)0.59167 (16)0.0759 (6)
H30.6532−0.07610.59110.091*
N50.8406 (2)0.16564 (13)0.57455 (13)0.0658 (5)
C20.8316 (2)−0.09943 (17)0.59504 (16)0.0596 (6)
C40.7147 (2)0.03782 (16)0.58914 (17)0.0668 (6)
C50.8282 (2)0.07584 (14)0.57999 (14)0.0555 (5)
C60.9311 (2)0.02398 (15)0.57896 (15)0.0585 (6)
H61.00300.05060.57270.070*
N60.93433 (16)0.28871 (10)0.33661 (12)0.0538 (4)
H6A1.00860.25450.35900.065*
N70.79767 (16)0.16933 (10)0.31325 (12)0.0503 (4)
H70.87420.14680.36670.060*
N80.67626 (16)0.29829 (10)0.24472 (12)0.0491 (4)
H80.67590.34110.21010.059*
C70.80155 (19)0.25245 (12)0.29824 (14)0.0464 (5)
C80.9677 (2)0.37724 (13)0.34492 (14)0.0539 (5)
C90.8938 (3)0.43773 (15)0.3642 (2)0.0768 (7)
H90.81840.42180.37320.092*
C100.9323 (4)0.52263 (18)0.3700 (2)0.1001 (10)
H100.88060.56390.38110.120*
C111.0463 (4)0.5467 (2)0.3594 (2)0.1051 (12)
H111.07180.60380.36320.126*
C121.1207 (3)0.4857 (2)0.3434 (2)0.0959 (10)
H121.19900.50150.33740.115*
C131.0833 (2)0.40133 (17)0.33588 (16)0.0702 (7)
H131.13560.36050.32470.084*
C140.67503 (19)0.11513 (11)0.24655 (15)0.0468 (5)
C150.6368 (3)0.05200 (14)0.28837 (19)0.0765 (7)
H150.68960.04520.35940.092*
C160.5197 (4)−0.00143 (18)0.2246 (2)0.1072 (11)
H160.4934−0.04460.25260.129*
C170.4422 (3)0.00873 (17)0.1204 (2)0.0877 (8)
H170.3628−0.02730.07760.105*
C180.4805 (2)0.07121 (15)0.07889 (18)0.0666 (6)
H180.42690.07810.00780.080*
C190.5977 (2)0.12417 (13)0.14139 (15)0.0535 (5)
H190.62500.16620.11270.064*
C200.54307 (19)0.28099 (11)0.24114 (14)0.0459 (5)
C210.5506 (2)0.26333 (14)0.33038 (16)0.0584 (5)
H210.64230.26160.39310.070*
C220.4205 (3)0.24817 (15)0.3260 (2)0.0725 (6)
H220.42440.23560.38580.087*
C230.2860 (3)0.25168 (17)0.2335 (2)0.0795 (7)
H230.19880.24110.23080.095*
C240.2785 (2)0.27057 (17)0.1450 (2)0.0760 (7)
H240.18640.27350.08260.091*
C250.4079 (2)0.28527 (14)0.14842 (16)0.0605 (6)
H250.40350.29800.08840.073*
U11U22U33U12U13U23
O20.0549 (9)0.0732 (11)0.0938 (12)0.0013 (8)0.0430 (8)−0.0117 (9)
O40.0486 (9)0.0987 (13)0.1444 (16)−0.0064 (8)0.0541 (10)−0.0593 (12)
O70.1289 (16)0.0814 (12)0.1126 (14)0.0391 (11)0.0908 (13)0.0146 (10)
O80.0851 (12)0.0926 (14)0.1211 (15)0.0113 (10)0.0675 (12)0.0081 (11)
N10.0447 (9)0.0748 (13)0.0567 (10)0.0156 (8)0.0290 (8)0.0017 (9)
N30.0438 (9)0.0791 (14)0.1104 (16)−0.0068 (9)0.0462 (10)−0.0360 (11)
N50.0622 (11)0.0797 (14)0.0520 (11)0.0232 (10)0.0293 (9)0.0050 (9)
C20.0385 (10)0.0779 (16)0.0564 (13)0.0058 (10)0.0224 (9)−0.0146 (12)
C40.0348 (10)0.0810 (17)0.0710 (14)0.0039 (10)0.0206 (10)−0.0295 (12)
C50.0441 (10)0.0706 (15)0.0443 (11)0.0153 (10)0.0196 (9)−0.0054 (10)
C60.0468 (11)0.0790 (16)0.0500 (12)0.0149 (10)0.0270 (9)0.0049 (11)
N60.0370 (8)0.0558 (10)0.0650 (10)−0.0021 (7)0.0260 (8)−0.0019 (8)
N70.0370 (8)0.0462 (9)0.0559 (10)0.0036 (7)0.0182 (7)0.0055 (7)
N80.0393 (8)0.0468 (9)0.0625 (10)0.0031 (7)0.0289 (7)0.0130 (8)
C70.0377 (10)0.0504 (12)0.0524 (11)−0.0005 (8)0.0257 (8)0.0006 (9)
C80.0458 (10)0.0578 (13)0.0475 (11)−0.0093 (9)0.0191 (9)−0.0011 (9)
C90.0752 (15)0.0629 (16)0.0913 (18)−0.0108 (12)0.0452 (14)−0.0139 (13)
C100.104 (2)0.0608 (17)0.101 (2)−0.0072 (16)0.0347 (18)−0.0097 (15)
C110.105 (2)0.070 (2)0.0763 (19)−0.0331 (18)0.0098 (17)0.0112 (15)
C120.0807 (19)0.105 (2)0.0703 (18)−0.0443 (18)0.0218 (15)0.0132 (16)
C130.0525 (12)0.0899 (18)0.0590 (13)−0.0203 (12)0.0249 (10)0.0025 (12)
C140.0392 (9)0.0431 (11)0.0566 (12)0.0040 (8)0.0256 (9)0.0000 (9)
C150.0956 (18)0.0578 (14)0.0655 (15)−0.0198 (13)0.0378 (13)0.0029 (11)
C160.137 (3)0.081 (2)0.092 (2)−0.0555 (19)0.057 (2)−0.0047 (16)
C170.0882 (18)0.0767 (18)0.088 (2)−0.0355 (14)0.0420 (16)−0.0208 (14)
C180.0613 (13)0.0670 (15)0.0630 (14)−0.0035 (11)0.0288 (11)−0.0089 (11)
C190.0505 (11)0.0527 (12)0.0600 (13)0.0007 (9)0.0321 (10)0.0009 (10)
C200.0417 (10)0.0421 (11)0.0577 (12)0.0052 (8)0.0299 (9)0.0059 (9)
C210.0543 (12)0.0613 (13)0.0646 (13)0.0073 (10)0.0359 (11)0.0101 (10)
C220.0781 (16)0.0782 (16)0.0897 (17)0.0069 (13)0.0643 (15)0.0110 (13)
C230.0579 (14)0.0906 (18)0.112 (2)−0.0022 (12)0.0608 (16)−0.0005 (15)
C240.0425 (11)0.1013 (19)0.0818 (17)0.0049 (11)0.0329 (11)−0.0025 (14)
C250.0440 (11)0.0753 (15)0.0620 (13)0.0082 (10)0.0291 (10)0.0074 (11)
O2—C21.231 (3)C11—C121.356 (4)
O4—C41.234 (2)C11—H110.9300
O7—N51.224 (2)C12—C131.369 (4)
O8—N51.233 (2)C12—H120.9300
N1—C61.322 (3)C13—H130.9300
N1—C21.362 (3)C14—C151.367 (3)
N3—C41.371 (3)C14—C191.375 (3)
N3—C21.379 (3)C15—C161.376 (3)
N3—H30.8600C15—H150.9300
N5—C51.422 (3)C16—C171.364 (4)
C4—C51.434 (3)C16—H160.9300
C5—C61.380 (3)C17—C181.356 (3)
C6—H60.9300C17—H170.9300
N6—C71.333 (2)C18—C191.368 (3)
N6—C81.422 (2)C18—H180.9300
N6—H6A0.8600C19—H190.9300
N7—C71.330 (2)C20—C251.373 (3)
N7—C141.425 (2)C20—C211.374 (3)
N7—H70.8600C21—C221.383 (3)
N8—C71.337 (2)C21—H210.9300
N8—C201.428 (2)C22—C231.368 (3)
N8—H80.8600C22—H220.9300
C8—C91.373 (3)C23—C241.367 (3)
C8—C131.378 (3)C23—H230.9300
C9—C101.383 (4)C24—C251.382 (3)
C9—H90.9300C24—H240.9300
C10—C111.375 (5)C25—H250.9300
C10—H100.9300
C6—N1—C2117.20 (18)C11—C12—C13121.5 (3)
C4—N3—C2127.8 (2)C11—C12—H12119.2
C4—N3—H3116.1C13—C12—H12119.2
C2—N3—H3116.1C12—C13—C8119.7 (3)
O7—N5—O8121.2 (2)C12—C13—H13120.2
O7—N5—C5119.5 (2)C8—C13—H13120.2
O8—N5—C5119.33 (18)C15—C14—C19119.88 (18)
O2—C2—N1122.85 (19)C15—C14—N7119.08 (18)
O2—C2—N3119.2 (2)C19—C14—N7121.02 (17)
N1—C2—N3117.9 (2)C14—C15—C16119.6 (2)
O4—C4—N3119.4 (2)C14—C15—H15120.2
O4—C4—C5129.0 (2)C16—C15—H15120.2
N3—C4—C5111.65 (18)C17—C16—C15120.2 (2)
C6—C5—N5118.7 (2)C17—C16—H16119.9
C6—C5—C4119.1 (2)C15—C16—H16119.9
N5—C5—C4122.10 (18)C18—C17—C16120.2 (2)
N1—C6—C5126.0 (2)C18—C17—H17119.9
N1—C6—H6117.0C16—C17—H17119.9
C5—C6—H6117.0C17—C18—C19120.2 (2)
C7—N6—C8127.70 (17)C17—C18—H18119.9
C7—N6—H6A116.1C19—C18—H18119.9
C8—N6—H6A116.1C18—C19—C14120.0 (2)
C7—N7—C14124.30 (15)C18—C19—H19120.0
C7—N7—H7117.8C14—C19—H19120.0
C14—N7—H7117.8C25—C20—C21120.68 (18)
C7—N8—C20124.48 (15)C25—C20—N8119.28 (18)
C7—N8—H8117.8C21—C20—N8119.99 (17)
C20—N8—H8117.8C20—C21—C22119.4 (2)
N7—C7—N6118.00 (16)C20—C21—H21120.3
N7—C7—N8121.24 (16)C22—C21—H21120.3
N6—C7—N8120.75 (17)C23—C22—C21119.9 (2)
C9—C8—C13119.7 (2)C23—C22—H22120.1
C9—C8—N6123.18 (19)C21—C22—H22120.1
C13—C8—N6117.1 (2)C24—C23—C22120.7 (2)
C8—C9—C10119.4 (3)C24—C23—H23119.7
C8—C9—H9120.3C22—C23—H23119.7
C10—C9—H9120.3C23—C24—C25119.9 (2)
C11—C10—C9120.7 (3)C23—C24—H24120.0
C11—C10—H10119.6C25—C24—H24120.0
C9—C10—H10119.6C20—C25—C24119.5 (2)
C12—C11—C10118.9 (3)C20—C25—H25120.3
C12—C11—H11120.5C24—C25—H25120.3
C10—C11—H11120.5
C6—N1—C2—O2−176.90 (19)C8—C9—C10—C11−1.8 (4)
C6—N1—C2—N32.8 (3)C9—C10—C11—C12−0.1 (4)
C4—N3—C2—O2173.4 (2)C10—C11—C12—C131.1 (4)
C4—N3—C2—N1−6.2 (3)C11—C12—C13—C8−0.2 (4)
C2—N3—C4—O4−174.6 (2)C9—C8—C13—C12−1.7 (3)
C2—N3—C4—C55.8 (3)N6—C8—C13—C12−179.87 (19)
O7—N5—C5—C6−169.02 (19)C7—N7—C14—C15−141.8 (2)
O8—N5—C5—C612.0 (3)C7—N7—C14—C1939.8 (3)
O7—N5—C5—C49.4 (3)C19—C14—C15—C16−0.8 (4)
O8—N5—C5—C4−169.6 (2)N7—C14—C15—C16−179.2 (2)
O4—C4—C5—C6178.0 (2)C14—C15—C16—C17−0.2 (5)
N3—C4—C5—C6−2.4 (3)C15—C16—C17—C180.4 (5)
O4—C4—C5—N5−0.4 (3)C16—C17—C18—C190.3 (4)
N3—C4—C5—N5179.21 (18)C17—C18—C19—C14−1.3 (3)
C2—N1—C6—C50.1 (3)C15—C14—C19—C181.5 (3)
N5—C5—C6—N1178.24 (18)N7—C14—C19—C18179.85 (18)
C4—C5—C6—N1−0.2 (3)C7—N8—C20—C25−136.65 (19)
C14—N7—C7—N6−152.77 (18)C7—N8—C20—C2145.7 (3)
C14—N7—C7—N826.0 (3)C25—C20—C21—C221.2 (3)
C8—N6—C7—N7−168.86 (18)N8—C20—C21—C22178.88 (19)
C8—N6—C7—N812.4 (3)C20—C21—C22—C23−0.6 (4)
C20—N8—C7—N731.5 (3)C21—C22—C23—C24−0.4 (4)
C20—N8—C7—N6−149.75 (18)C22—C23—C24—C250.8 (4)
C7—N6—C8—C934.2 (3)C21—C20—C25—C24−0.8 (3)
C7—N6—C8—C13−147.7 (2)N8—C20—C25—C24−178.5 (2)
C13—C8—C9—C102.7 (3)C23—C24—C25—C20−0.2 (4)
N6—C8—C9—C10−179.3 (2)
D—H···AD—HH···AD···AD—H···A
N6—H6A···O2i0.861.942.794 (2)174
N7—H7···N1i0.862.212.934 (2)142
N8—H8···O4ii0.862.052.887 (2)163
Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯AD—HH⋯ADAD—H⋯A
N6—H6A⋯O2i0.861.942.794 (2)174
N7—H7⋯N1i0.862.212.934 (2)142
N8—H8⋯O4ii0.862.052.887 (2)163

Symmetry codes: (i) ; (ii) .

  3 in total

1.  Structural determinants of sigma receptor affinity.

Authors:  B L Largent; H Wikström; A L Gundlach; S H Snyder
Journal:  Mol Pharmacol       Date:  1987-12       Impact factor: 4.436

2.  A short history of SHELX.

Authors:  George M Sheldrick
Journal:  Acta Crystallogr A       Date:  2007-12-21       Impact factor: 2.290

3.  1,3-Di(2-[5-3H]tolyl)guanidine: a selective ligand that labels sigma-type receptors for psychotomimetic opiates and antipsychotic drugs.

Authors:  E Weber; M Sonders; M Quarum; S McLean; S Pou; J F Keana
Journal:  Proc Natl Acad Sci U S A       Date:  1986-11       Impact factor: 11.205

  3 in total

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